public class IonFactory extends Object
Modifier and Type | Method and Description |
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static ArrayList<NeutralLoss> |
getDefaultNeutralLosses()
Returns the default neutral losses.
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HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Peptide peptide)
This method returns all the theoretic ions expected from a peptide.
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HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Peptide peptide,
SpecificAnnotationSettings specificAnnotationSettings)
This method returns the theoretic ions expected from a peptide.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Tag tag)
This method returns the theoretic ions expected from a tag.
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static IonFactory |
getInstance()
Static method which returns the instance of the factory.
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static double |
getLossesMass(ArrayList<NeutralLoss> neutralLosses)
Convenience summing the masses of various neutral losses.
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static ArrayList<NeutralLoss> |
getNeutralLosses(PtmSettings ptmSettings)
Returns a list containing the default neutral losses and the losses found
in the given modifications.
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NeutralLossCombination[] |
getNeutralLossesCombinations(ArrayList<NeutralLoss> possibleNeutralLosses)
Returns the possible neutral losses combinations as array of arrays of
neutral losses.
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static HashSet<Integer> |
getReporterIons(PtmSettings ptmSettings)
Returns the reporter ions to annotate with the given PTM settings.
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public static IonFactory getInstance()
public static ArrayList<NeutralLoss> getDefaultNeutralLosses()
public static ArrayList<NeutralLoss> getNeutralLosses(PtmSettings ptmSettings)
ptmSettings
- the PTM settingspublic static HashSet<Integer> getReporterIons(PtmSettings ptmSettings)
ptmSettings
- the PTMs to annotatepublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Peptide peptide)
peptide
- The considered peptidepublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Peptide peptide, SpecificAnnotationSettings specificAnnotationSettings)
peptide
- The considered peptidespecificAnnotationSettings
- if provided, only the ions detectable
using these settings will be selectedpublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Tag tag)
tag
- the considered tagpublic NeutralLossCombination[] getNeutralLossesCombinations(ArrayList<NeutralLoss> possibleNeutralLosses)
possibleNeutralLosses
- the possible neutral losses to includepublic static double getLossesMass(ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- list of neutral lossesCopyright © 2018. All rights reserved.